Colin Kaepernick, five months after exploring a trade to the Denver Broncos, walked off their practice field Wednesday as if he was the most popular guy in town, even if he was still in a 49ers uniform.

Never mind that he didn’t throw a single pass during the formal practice with the Broncos — he briefly threw on a side field — or that his only action in team drills featured three handoffs, which has been his typical workload the past week because of a sore shoulder.

Broncos and 49ers fans clamored for his autograph afterward, and he obliged for some 20 minutes, despite security officials trying to usher him off to the locker room. One fan, in a Kaepernick replica jersey, actually swatted arms with the Broncos security officer escorting Kaepernick, and when a sheriff deputy intervened, Kaepernick immediately stepped in to cool all parties.

General manager Trent Baalke isn’t willing to rush Kaepernick back from a “fatigued” arm for popularity sake, or for the starting competition with Blaine Gabbert.

“This is just a young man that went out and his arm is tired,” Baalke said. “Rather than push it any further, back it down, give him a little time to rest it. We don’t have to be ready to play a game just yet. This is preseason football.”

What a bizarre scene it was, watching fans of both teams beg for his autograph. “Niner for life!” one shouted at Kaepernick. “We’ll see about that,” responded a Broncos fan. Some 5,000 fans attended the public practice.

In March, Kaepernick visited with Broncos general manager John Elway and coach Gary Kubiak, a month after Kaepernick’s agents requested permission from the 49ers to seek a trade. The Broncos were interested to a point. Kaepernick was unwilling to take a significant pay cut from his $11.9 million base salary that became guaranteed April 1, and the 49ers were unwilling to defray the costs.

Kaepernick may be missing practice reps but he’s been a daily presence since April. Contributing to his recent arm fatigue was his inability to throw in the offseason because of his rehabilitation from multiple surgeries (left shoulder, left knee, right thumb).

Kaepernick’s latest issue, which he described as tightness in his shoulder, does not require surgery, a league source said.

“His arm’s tired,” Baalke added. “To say it’s dead, I wouldn’t make that assumption. … He just needed a little time to give it a rest.”

Baalke expects Kaepernick to throw some Thursday when the 49ers again visit the Broncos facility, though it’s unknown whether that will be against the Broncos defense or merely on a side field like Wednesday.

Kaepernick had been splitting first-team reps with Blaine Gabbert the first nine practices in training camp. But Kaepernick stopped throwing after last Wednesday’s session at Kezar Stadium.

Interestingly, Christian Ponder said the 49ers first contacted him Friday, and he signed four days later, after Thad Lewis’ knee injury further depleted the corps of healthy arms. Ponder did not have a workout and simply passed a physical before signing.

For the past week, Kaepernick has reverted to his offseason-program mode of shadowing other quarterbacks and occasionally participating in run-only plays. On Wednesday, he also gave a tutorial on the sideline to a trio of young running backs about handoffs.

Gabbert completed 4-of-7 passes in full-team drills, but his last one got intercepted and his offensive line repeatedly couldn’t keep Broncos pass rushers from penetrating for would-be sacks. Gabbert also had a pass bounce off DiAndre Campbell’s hands and into linebacker Todd Davis’ for an interception in seven-on-seven rills.

Ponder and Jeff Driskel each had their last pass intercepted in 11-on-11 drills, and those came shortly after Gabbert’s finale.

Ponder practiced as the third-string quarterback and is cramming to learn the playbook as he expects to play Saturday night.

Ponder didn’t play last season, though he was in training camp with the Raiders and spent two games on the Denver Broncos’ inactive list. Once NFL offseason programs began in April, Ponder said, “I started working out in my garage, every now and again, and not as much as I should have. I had a quarterback net in the front yard. It was real old school.”

Said Modkins: “I’ve known Christian since he was in high school. I recruited him when I was at Georgia Tech and he broke my heart back then and went to Florida State. I reminded him of that when I saw him. But, he’ll be fine. He’s smart. He’s athletic. He’ll be able to do the things we ask him to do and I expect him to be able to catch up to speed pretty quickly.”

— What was it like to practice against reigning Super Bowl champions? “They’re a great team that knows how to practice and how to win,” safety Antoine Bethea said. “Us being a young team, by practicing these two days against them, it’s going to pay dividends.”

— To help acclimate to the mile-high altitude and also work out against unfamiliar foes, the 49ers are practicing back-to-back days with the host Broncos ahead of Saturday night’s exhibition. The teams followed the same schedule a year ago at the Broncos’ facility in Englewood, Colorado. “You feel (the altitude) in individuals and sprints,” linebacker NaVorro Bowman said. “It’ll help us on Sunday.”

— Jimmie Ward gave up a long touchdown pass from Mark Sanchez to Emmanuel Sanders that drew the crowd’s biggest applause of the day.

— Outside linebacker Aaron Lynch and Broncos first-year center Dillon Day got in a brief melee during which their helmets were ripped from their heads. Another minor scuffle broke out minutes later between those on the 49ers defense and Broncos offense, while no similar incidents occurred on the neighboring field between the 49ers offense and Broncos defense.

— Defensive tackle Arik Armstead (shoulder) worked with Hall of Famer Charles Haley on pass-rush moves. Haley has been assisting the defensive linemen for the past week. Armstead was otherwise limited Wednesday to individual conditioning with a strength coach.

— Wide receivers Bruce Ellington and DeAndre Smelter, who are believed to be battling leg injuries, practiced. Ellington stretched with the team.

— The most noticeable injury came when Broncos defensive end Derek Wolfe injured his left leg while rushing the pocket on a Gabbert completion to Vance McDonald.